SumVg: Total Heritability Explained by All Variants in Genome-Wide Association Studies Based on Summary Statistics with Standard Error Estimates

Abstract

Genome-wide association studies (GWAS) are commonly employed to study the genetic basis of complex traits/diseases, and a key question is how much heritability could be explained by all single nucleotide polymorphisms (SNPs) in GWAS. One widely used approach that relies on summary statistics only is linkage disequilibrium score regression (LDSC); however, this approach requires certain assumptions about the effects of SNPs (e.g., all SNPs contribute to heritability and each SNP contributes equal variance). More flexible modeling methods may be useful. We previously developed an approach recovering the “true” effect sizes from a set of observed z-statistics with an empirical Bayes approach, using only summary statistics. However, methods for standard error (SE) estimation are not available yet, limiting the interpretation of our results and the applicability of the approach. In this study, we developed several resampling-based approaches to estimate the SE of SNP-based heritability, including two jackknife and three parametric bootstrap methods. The resampling procedures are performed at the SNP level as it is most common to estimate heritability from GWAS summary statistics alone. Simulations showed that the delete-d-jackknife and parametric bootstrap approaches provide good estimates of the SE. In particular, the parametric bootstrap approaches yield the lowest root-mean-squared-error (RMSE) of the true SE. We also explored various methods for constructing confidence intervals (CIs). In addition, we applied our method to estimate the SNP-based heritability of 12 immune-related traits (levels of cytokines and growth factors) to shed light on their genetic architecture. We also implemented the methods to compute the sum of heritability explained and the corresponding SE in an R package SumVg. In conclusion, SumVg may provide a useful alternative tool for calculating SNP heritability and estimating SE/CI, which does not rely on distributional assumptions of SNP effects.